/**
* Execute the algorithm.
*/
void LoadSassena::exec()
{
//auto gws=boost::dynamic_pointer_cast<API::WorkspaceGroup>(getProperty("OutputWorkspace"));
//API::WorkspaceGroup_sptr gws=getProperty("OutputWorkspace");
API::Workspace_sptr ows=getProperty("OutputWorkspace");
API::WorkspaceGroup_sptr gws=boost::dynamic_pointer_cast<API::WorkspaceGroup>(ows);
if(gws && API::AnalysisDataService::Instance().doesExist( gws->name() ) )
{
//gws->deepRemoveAll(); // remove workspace members
API::AnalysisDataService::Instance().deepRemoveGroup( gws->name() );
}
else
{
gws = boost::make_shared<API::WorkspaceGroup>();
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<API::Workspace>(gws));
}
//populate m_validSets
int nvalidSets = 4;
const char* validSets[] = { "fq", "fq0", "fq2", "fqt"};
for(int iSet=0; iSet<nvalidSets; iSet++) this->m_validSets.push_back( validSets[iSet] );
//open the HDF5 file for reading
m_filename = this->getPropertyValue("Filename");
hid_t h5file = H5Fopen(m_filename.c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
if( h5file < 0)
{
this->g_log.error("Cannot open "+m_filename);
throw Kernel::Exception::FileError("Unable to open:" , m_filename);
}
//find out the sassena version used
char cversion[16];
if ( H5LTget_attribute_string( h5file, "/", "sassena_version", cversion ) < 0 )
{
this->g_log.error("Unable to read Sassena version");
}
//const std::string version(cversion);
//determine which loader protocol to use based on the version
//to be done at a later time, maybe implement a Version class
std::vector<int> sorting_indexes;
const MantidVec qvmod = this->loadQvectors( h5file, gws, sorting_indexes);
//iterate over the valid sets
std::string setName;
for(std::vector<std::string>::const_iterator it=this->m_validSets.begin(); it!=this->m_validSets.end(); ++it){
setName = *it;
if(H5LTfind_dataset(h5file,setName.c_str())==1)
{
if(setName == "fq" || setName == "fq0" || setName == "fq2")
this->loadFQ( h5file, gws, setName, qvmod, sorting_indexes);
else if(setName == "fqt")
this->loadFQT( h5file, gws, setName, qvmod, sorting_indexes);
}
else
this->g_log.information("Dataset "+setName+" not present in file");
}// end of iterate over the valid sets
H5Fclose(h5file);
} // end of LoadSassena::exec()
/* ------- begin -------------------------- readConvergence.c --- */
void readConvergence(void) {
/* This is a self-contained function to read the convergence matrix,
written by RH. */
const char routineName[] = "readConvergence";
char *atmosID;
int ncid, ncid_mpi, nx, ny;
size_t attr_size;
hid_t plist;
H5T_class_t type_class;
mpi.rh_converged = matrix_int(mpi.nx, mpi.ny);
/* --- Open the inputdata file --- */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Get ncid of the MPI group */
if (( ncid_mpi = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, "/", "nx", &nx) ) < 0) HERR(routineName);
if (nx != mpi.nx) {
sprintf(messageStr,
"Number of x points mismatch: expected %d, found %d.",
mpi.nx, (int)nx);
Error(WARNING, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid, "/", "ny", &ny) ) < 0) HERR(routineName);
if (ny != mpi.ny) {
sprintf(messageStr,
"Number of y points mismatch: expected %d, found %d.",
mpi.ny, (int)ny);
Error(WARNING, routineName, messageStr);
}
/* --- Read variable --- */
if (( H5LTread_dataset_int(ncid_mpi, CONV_NAME,
mpi.rh_converged[0]) ) < 0) HERR(routineName);
/* --- Close inputdata file --- */
if (( H5Gclose(ncid_mpi) ) < 0) HERR(routineName);
if (( H5Fclose(ncid) ) < 0) HERR(routineName);
return;
}
int_f
h5ltget_attribute_string_c(hid_t_f *loc_id,
size_t_f *namelen,
_fcd dsetname,
size_t_f *attrnamelen,
_fcd attrname,
_fcd buf, size_t_f *buf_size)
{
int ret_value = -1;
herr_t ret;
char *c_name = NULL;
char *c_attrname = NULL;
char *c_buf = NULL;
/*
* Convert FORTRAN name to C name
*/
c_name = (char *)HD5f2cstring(dsetname, (size_t)*namelen);
if (c_name == NULL)
goto done;
c_attrname = (char *)HD5f2cstring(attrname, (size_t)*attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* Allocate buffer to hold C attribute string
*/
if ((c_buf = (char *)HDmalloc((size_t)*buf_size + 1)) == NULL)
goto done;
/*
* Call H5LTget_attribute_int function.
*/
ret = H5LTget_attribute_string((hid_t)*loc_id,c_name,c_attrname,c_buf);
if (ret < 0)
goto done;
/*
* Convert C name to FORTRAN and place it in the given buffer
*/
HD5packFstring(c_buf, _fcdtocp(buf), (size_t)*buf_size);
ret_value = 0;
done:
if(c_name!=NULL)
HDfree(c_name);
if(c_attrname!=NULL)
HDfree(c_attrname);
if(c_buf!=NULL)
HDfree(c_buf);
return ret_value;
}
int_f
nh5ltget_attribute_string_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
int c_namelen;
int c_attrnamelen;
/*
* Convert FORTRAN name to C name
*/
c_namelen = (int)*namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL)
goto done;
c_attrnamelen = (int)*attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* Call H5LTget_attribute_int function.
*/
c_loc_id = (hid_t)*loc_id;
ret = H5LTget_attribute_string(c_loc_id,c_name,c_attrname,buf);
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
free(c_name);
if(c_attrname!=NULL)
free(c_attrname);
return ret_value;
}
/**
* Read integer attribute.
*
* @param [in] DatasetName
* @param [in] AttributeName
* @return Attribute value
* @throw ios::failure
*/
inline string THDF5_File::ReadStringAttribute(const char * DatasetName, const char * AttributeName){
char Value[256] = "";
herr_t status = H5LTget_attribute_string (HDF5_FileId, DatasetName, AttributeName, Value);
if (status < 0) {
char ErrorMessage[256];
sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotReadFromAttribute,AttributeName, DatasetName);
throw ios::failure(ErrorMessage);
}
return Value;
}// end of ReadIntAttribute
int pioReadAttributeString(PIOObject pioObject,
const char* attr_name, char** attr_value)
{
hid_t attr;
size_t storage;
if (pioHasAttribute(pioObject, attr_name))
{
attr = H5Aopen_name(pioObject.identifier, attr_name);
storage = H5Aget_storage_size(attr);
H5Aclose(attr);
*attr_value = (char*)malloc( storage + sizeof(char));
H5LTget_attribute_string(pioObject.identifier, ".",
attr_name, *attr_value);
return 1;
}
else {
return -1;
}
}
int SpIO_H5GetAttribute_string(hid_t h5f_id, const char *obj_name, const char *attr_name, char **attribute)
{
int status = 0;
herr_t hstatus = 0;
hsize_t dims;
H5T_class_t class;
size_t size;
if(hstatus >= 0)
hstatus = H5LTget_attribute_info(h5f_id, obj_name, attr_name, &dims, &class, &size);
if(hstatus >= 0) {
*attribute = Mem_CALLOC(size, *attribute);
hstatus = H5LTget_attribute_string(h5f_id, obj_name, attr_name, *attribute);
}
if(hstatus < 0) {
PyWrErr_SetString(PyExc_Exception, "Error getting attribute '%s' from '%s'", attr_name, obj_name);
status = 1;
}
return status;
}
/* ------- begin -------------------------- readMolPops_p.c -- */
void readMolPops(Molecule *molecule) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
-- -------------- */
const char routineName[] = "readMolPops";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open molecule group --- */
sprintf(group_name, "molecule_%s", molecule->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = molecule->Nv;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = molecule->Nv;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, molecule->nv[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- readPopulations_p.c -- */
void readPopulations(Atom *atom) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
Note2: This routine will not work yet in HFD5. Access to the aux file
needs to be better regulated in OLD_POPULATIONS cases (ie, append
and read/write acess). The code below assumes the file is already
open, which may not be the case.
-- -------------- */
const char routineName[] = "readPopulations_p";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = atom->Nlevel;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = atom->Nlevel;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atom->n[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------- init_aux_existing.c --- */
void init_aux_existing(void) {
const char routineName[] = "init_aux_existing";
int i, nlevel, nline, ncont;
size_t attr_size;
hid_t ncid, ncid_atom, ncid_mol, plist;
H5T_class_t type_class;
char group_name[ARR_STRLEN], *atmosID;
Atom *atom;
Molecule *molecule;
/* Open the file with parallel MPI-IO access */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(AUX_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
io.aux_ncid = ncid;
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* --- Get ncid of the atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( io.aux_atom_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_atom = io.aux_atom_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_atom, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "nline", &nline) ) < 0)
HERR(routineName);
if (nline != atom->Nline) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
atom->Nline, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "ncontinuum", &ncont) ) < 0)
HERR(routineName);
if (ncont != atom->Ncont) {
sprintf(messageStr,
"Number of continua mismatch: expected %d, found %d.",
atom->Ncont, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_atom_pop[i] = H5Dopen(ncid_atom, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_poplte[i] = H5Dopen(ncid_atom, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
if (( io.aux_atom_RijL[i] = H5Dopen(ncid_atom, RIJ_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiL[i] = H5Dopen(ncid_atom, RJI_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( io.aux_atom_RijC[i] = H5Dopen(ncid_atom, RIJ_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiC[i] = H5Dopen(ncid_atom, RJI_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
}
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* --- Get ncid of the molecule group --- */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( io.aux_mol_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_mol = io.aux_mol_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_mol, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nline_molecule", &nline) ) < 0)
HERR(routineName);
if (nline != molecule->Nrt) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
molecule->Nrt, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nJ", &ncont) ) < 0)
HERR(routineName);
if (ncont != molecule->NJ) {
sprintf(messageStr,
"Number of J mismatch: expected %d, found %d.",
molecule->NJ, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_mol_pop[i] = H5Dopen(ncid_mol, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_mol_poplte[i] = H5Dopen(ncid_mol, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
} /* end active MOLECULES loop */
return;
}
/* ------- begin -------------------------- init_hdf5_indata_old.c --- */
void init_hdf5_indata_existing(void)
/* Opens an existing NetCDF input data file, loads structures and ids */
{
const char routineName[] = "init_hdf5_indata_existing";
int ncid;
size_t attr_size;
hid_t plist;
char *atmosID;
H5T_class_t type_class;
/* Open the file with parallel MPI-IO access */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
io.in_ncid = ncid;
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Get group IDs */
if (( io.in_input_ncid = H5Gopen(ncid, "input", H5P_DEFAULT) ) < 0)
HERR(routineName);
if (( io.in_atmos_ncid = H5Gopen(ncid, "atmos", H5P_DEFAULT) ) < 0)
HERR(routineName);
if (( io.in_mpi_ncid = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Open datasets collectively ---*/
if (( io.in_atmos_T = H5Dopen(io.in_atmos_ncid, "temperature",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dopen(io.in_atmos_ncid, "velocity_z",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dopen(io.in_atmos_ncid, "height",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dopen(io.in_mpi_ncid, TASK_MAP,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dopen(io.in_mpi_ncid, TASK_NUMBER,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dopen(io.in_mpi_ncid, ITER_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dopen(io.in_mpi_ncid, CONV_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dopen(io.in_mpi_ncid, DM_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dopen(io.in_mpi_ncid, DMH_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dopen(io.in_mpi_ncid, ZC_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
return;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
void rdiff(const char *name, hid_t f1, hid_t f2) {
hid_t g1 = H5Gopen(f1, name, H5P_DEFAULT);
hid_t g2 = H5Gopen(f2, name, H5P_DEFAULT);
if (g1 >= 0 && g2 >= 0) {
int n1 = H5Aget_num_attrs(g1);
for (int i = 0; i < n1; i++) {
char aname[MAXNAME];
hid_t a1 = H5Aopen_idx(g1, i);
assert(H5Aget_name(a1, MAXNAME, aname) < MAXNAME);
H5Aclose(a1);
if (!H5LTfind_attribute(g2, aname)) {
printf("Only in %s[%s%s]\n", file1, name, aname);
continue;
}
int d1, d2;
H5LTget_attribute_ndims(f1, name, aname, &d1);
H5LTget_attribute_ndims(f2, name, aname, &d2);
assert(d1 <= 1 && d2 <= 1);
hsize_t dims1, dims2;
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_attribute_info(f1, name, aname, &dims1, &t1, &ts1);
H5LTget_attribute_info(f2, name, aname, &dims2, &t2, &ts2);
assert(t1 == t2);
assert(t1 == H5T_INTEGER || t1 == H5T_FLOAT || t1 == H5T_STRING);
if (t1 == H5T_INTEGER) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
int v1, v2;
H5LTget_attribute_int(f1, name, aname, &v1);
H5LTget_attribute_int(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%d %s[%s%s]=%d\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_FLOAT) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
float v1, v2;
H5LTget_attribute_float(f1, name, aname, &v1);
H5LTget_attribute_float(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%g %s[%s%s]=%g\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_STRING) {
assert(ts1 < 256 && ts2 < 256);
char buf1[256];
char buf2[256];
H5LTget_attribute_string(f1, name, aname, buf1);
H5LTget_attribute_string(f2, name, aname, buf2);
if (strcmp(buf1, buf2)) {
printf("%s[%s%s]=%s %s[%s%s]=%s\n", file1, name, aname, buf1, file2, name, aname, buf2);
}
}
}
int n2 = H5Aget_num_attrs(g2);
for (int i = 0; i < n2; i++) {
char aname[MAXNAME];
hid_t a2 = H5Aopen_idx(g2, i);
assert(H5Aget_name(a2, MAXNAME, aname) < MAXNAME);
H5Aclose(a2);
if (!H5LTfind_attribute(g1, aname)) {
printf("Only in %s[%s%s]\n", file2, name, aname);
continue;
}
}
hsize_t nobj;
H5Gget_num_objs(g1, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g1, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g1, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g2, oname)) {
printf("Only in %s[%s%s]\n", file1, name, oname);
continue;
}
hsize_t dims1[2], dims2[2];
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_dataset_info(g1, oname, dims1, &t1, &ts1);
H5LTget_dataset_info(g2, oname, dims2, &t2, &ts2);
if (dims1[0] != dims2[0] || dims1[1] != dims2[1]) {
printf("%s[%s%s](%d,%d) != %s[%s%s](%d,%d)\n",
file1, name, oname, dims1[1], dims1[0],
file2, name, oname, dims2[1], dims2[0]);
continue;
}
float *data1 = malloc(dims1[0]*dims1[1]*sizeof(float));
float *data2 = malloc(dims1[0]*dims1[1]*sizeof(float));
H5LTread_dataset_float(g1, oname, data1);
H5LTread_dataset_float(g2, oname, data2);
float maxdiff = 0;
for (int i = dims1[0]*dims1[1]-1; i >= 0; i--) {
float d = data1[i] - data2[i];
if (d < 0) d = -d;
if (d > maxdiff) maxdiff = d;
}
printf("max |%s[%s%s] - %s[%s%s]| = %g\n",
file1, name, oname, file2, name, oname, maxdiff);
free(data1); free(data2);
}
H5Gget_num_objs(g2, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g2, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g2, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g1, oname)) {
printf("Only in %s[%s%s]\n", file2, name, oname);
continue;
}
}
H5Gclose(g1);
H5Gclose(g2);
} else if (g1 >= 0) {
printf("Only in %s:%s\n", file1, name);
H5Gclose(g1);
} else if (g2 >= 0) {
printf("Only in %s:%s\n", file2, name);
H5Gclose(g2);
} else {
printf("Group %s does not exist in either file.\n", name);
}
}